Files in kevinlkx/mapgen

Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

Mapgen.Rproj

NAMESPACE

R/annots.R R/development.R R/diagnosis.R R/finemapping.R R/gene_mapping.R R/gwas.R R/harmonization.R R/partition_pips.R R/plots.R R/torus.R R/utils-pipe.R R/utils.R README.Rmd README.md

_pkgdown.yml

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/data_preparation_tutorial.html

docs/articles/data_preparation_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/enrichment_tutorial.html

docs/articles/enrichment_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/finemapping_tutorial.html

docs/articles/finemapping_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/finemapping_ukbb_ld_diagnosis.html

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docs/articles/gene_mapping_tutorial.html

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docs/articles/gene_mapping_tutorial_files/figure-html/gene-manhattan-plot-1.png

docs/articles/index.html

docs/articles/make_trackplots.html

docs/articles/make_trackplots_files/figure-html/make-CALU-trackplot-1.png

docs/articles/make_trackplots_files/figure-html/make-HCN4-trackplot-1.png

docs/articles/partition_pip_tutorial.html

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docs/articles/partition_pip_tutorial_files/figure-html/structure-plot-OCRs-1.png

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docs/articles/track_plot_tutorial.html

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docs/authors.html

docs/bootstrap-toc.css

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docs/docsearch.css

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docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/LD_diagnosis_rss.html

docs/reference/LD_diagnosis_susie_rss.html

docs/reference/Rplot001.png

docs/reference/annotate_snps_binary.html

docs/reference/annotator_merged.html

docs/reference/assign_locus_snp.html

docs/reference/assign_snp_locus.html

docs/reference/block_view_summary.html

docs/reference/clean_sumstats.html

docs/reference/compile_structure_plot_data.html

docs/reference/compute_distance_weight.html

docs/reference/compute_gene_pip.html

docs/reference/extract_gene_level_result.html

docs/reference/figures/gene.mapping.diagram.png

docs/reference/figures/workflow.overview.png

docs/reference/find_nearest_genes.html

docs/reference/finemapping_annot_trackplot.html

docs/reference/gene_by_distance.html

docs/reference/gene_cs.html

docs/reference/gene_manhattan_plot.html

docs/reference/gene_view_summary.html

docs/reference/get_UKBB_region_info.html

docs/reference/get_gene_cs.html

docs/reference/get_locus_level_gene_pip.html

docs/reference/get_nearby_interactions.html

docs/reference/harmonize_sumstats_LD.html

docs/reference/index.html

docs/reference/load_UKBB_LDREF.html

docs/reference/make_genomic_annots.html

docs/reference/make_structure_plot.html

docs/reference/match_gwas_LDREF.html

docs/reference/match_gwas_bigsnp.html

docs/reference/merge_bigsnp_gwas.html

docs/reference/merge_susie_sumstats.html

docs/reference/nearby_interactions.html

docs/reference/partition_pip_annots.html

docs/reference/partition_pip_regions.html

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docs/reference/pipe.html

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docs/reference/prepare_torus_input_files.html

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docs/reference/process_pcHiC.html

docs/reference/read_LD.html

docs/reference/read_LD_SNP_info.html

docs/reference/run_finemapping.html

docs/reference/run_susie.html

docs/reference/run_susie_rss.html

docs/reference/run_torus.html

docs/reference/snp_view_summary.html

docs/reference/structure_plot.html

docs/reference/sum_pip_annots.html

docs/reference/sum_pip_regions.html

docs/reference/susie_finemap_region.html

docs/reference/track_plot.html

docs/sitemap.xml

inst/extdata/AF.finemapping.sumstats.rds

inst/extdata/LD.blocks.EUR.hg19.rds

inst/extdata/OCRs.hg19.gr.rds

inst/extdata/disjoint.OCRs.hg19.grlist.rds

inst/extdata/genomic.annots.hg19.rds

inst/extdata/heart_ventricle-ENCODE_ABC.tsv.gz

inst/extdata/pcHiC.CM.gr.rds

inst/extdata/test.processed.sumstats.rds

inst/extdata/test.sumstats.txt.gz

inst/extdata/test.torus.res.rds

inst/extdata/test_bed_dir/testbed.bed

inst/extdata/test_bed_dir/testbed2.bed

man/LD_diagnosis_susie_rss.Rd man/assign_snp_locus.Rd man/block_view_summary.Rd man/clean_sumstats.Rd man/compute_gene_pip.Rd man/extract_gene_level_result.Rd

man/figures/gene.mapping.diagram.png

man/figures/workflow.overview.png

man/find_nearest_genes.Rd man/gene_cs.Rd man/gene_manhattan_plot.Rd man/gene_view_summary.Rd man/get_UKBB_region_info.Rd man/get_locus_level_gene_pip.Rd man/harmonize_sumstats_LD.Rd man/load_UKBB_LDREF.Rd man/make_genomic_annots.Rd man/match_gwas_LDREF.Rd man/match_gwas_bigsnp.Rd man/merge_susie_sumstats.Rd man/nearby_interactions.Rd man/partition_pip_annots.Rd man/partition_pip_regions.Rd man/pip_structure_plot.Rd man/pipe.Rd man/prepare_susie_data_with_torus_result.Rd man/prepare_torus_input_files.Rd man/process_ABC.Rd man/process_finemapping_sumstats.Rd man/process_gwas_sumstats.Rd man/process_loop_data.Rd man/process_pcHiC.Rd man/read_LD.Rd man/read_LD_SNP_info.Rd man/run_finemapping.Rd man/run_torus.Rd man/snp_view_summary.Rd man/susie_finemap_region.Rd man/track_plot.Rd vignettes/data_preparation_tutorial.Rmd vignettes/enrichment_tutorial.Rmd vignettes/finemapping_tutorial.Rmd vignettes/finemapping_ukbb_ld_diagnosis.Rmd vignettes/gene_mapping_tutorial.Rmd vignettes/partition_pip_tutorial.Rmd vignettes/track_plot_tutorial.Rmd

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.